GENOME ANALYSIS REPORT

Data used in this analysis

In this experiment, the start set data are:

• Problem genomes, that are complete genome for probiotic Shewanella. sp Pdp11 and scaffold for SdM1, SdM2, SH4, SH12, SH6, SH9 strains
• 16S RNA gene sequence (ab1 file)

GENERAL DESCRIPTION

This report shows all the genome analysis information including:

• 16S RNA identification
• Complete genome annotation by Dfast Tool
• Genome comparison with other complete Shewanella genomes described on NCBI assignation by Pyani (https://github.com/widdowquinn/pyani) and Synteny blocks comparison Sibelia
• Transposon identification (Tp)
• Genomic island identification (GIs) and enrichment analysis
• Genome comparison with shewanella pathogenic strains by Tarsynflow (https://github.com/seoanezonjic/TarSynFlow)

The taxonomy identification of problem strains as Shewanella genus was based on Silva Taxonomy results (https://www.arb-silva.de/documentation/silva-taxonomy/). The species was identified by blastn of 16S RNA gene and the problematic strain genomes comparison with 120 complete genomes described on NCBI database. The complete genome of Shewanella. sp Pdp11 and partial genome of pathogenic and saprophyte strains of Shewanella were annotated using the Dfast tool, by Clusters of Orthologous Groups (COG) and the number of genes associated with categories were determined. The transposons have been detected by the ISEScan tool (https://github.com/xiezhq/ISEScan) which was complemented with tp_finder workflow for transposase and disrupt protein identification. The genomic islands were identified using IslandViewer 4 software and the GI enrichment was analysed by DEgenes Hunter (https://github.com/seoanezonjic/ExpHunterSuite), by API option. The genome comparison of Shewanella.sp Pdp11 and pathogenic strains allow us to identify specific genes of pathogenic strains and their absence in probiotic strain.

16S RNA

The Table indicated the 16S RNA analysis of problem genomes was carried out by blatn. The top 10 for each strain with high identity and coverage value.

Complete genome comparison

Heatmaps represent the calculation of the Average Nucleotide Identity (ANI) by MUMmer (NUCmer) to align the input sequences, giving us as results the specific nucleotide identity (first heatmap) and coverage (second heatmap) of 0 to 1 value, between our 8 strains studies and 129 complete genomes of the Shewanella genus available at NCBI. The probiotic Shewanella Pdp11 had a high identity and coverage with Shewanella baltica genus, SH4 and SH12 with Shewanella xiamenensis, while SH6, SH16, SH9 and SdM1 have similarity with Shewanella oncorhynchi

Sybelia results

Synteny blocks of Shewanella Pdp 11 with S. baltica 128 (left) and S. putrefaciens 4H(right)

Genome annotation

The Dfast tool (https://dfast.ddbj.nig.ac.jp/) was used for the 137 complete genomes COG annotation. The heatmaps represent the number of genes associated with a COG functional category (left heatmap) and the number of genes standardization with each genome's number of Coding Sequence (CDS) represented in genes percent (gene %) (right heatmap).

Transposon

The Transposable elements (TEs) identification in 137 complete genomes was carried out by custom workflow using ISEScan(https://github.com/xiezhq/ISEScan) and Tp finder. The results showed the number of TEs identified in each genome (left barplot), the number of TEs standardized concerning several Coding Sequence (CDS) (right barplot ), as well as the repeat TEs inside the genome (Table). The presence or absence of disrupted proteins (left heatmap) and transposases (right Heatmap) at each genome was also determined, represented by a matrix of 0 and 1.

Genomic Island

The Mobilome analysis included the genomic island (GI) identification using IslandViewer4 (https://www.pathogenomics.sfu.ca/islandviewer/). Results shows the total of GIs identified at 137 research strains of Shewanella.sp. The Figure shows the number of genomic islands in which some functional categories are significant, determined by Dfast. The GIs were identified in 137 research strains of Shewanella.sp. Additionally, the COG categories functional enrichment was accomplished by ExpHunterSuite script clusters_to_enrichment.R, which is based on the clusterProfiler package, with FDR threshold (-p 0.05). The heatmap represents the number of GI included in COG categories (left) and this number was proportioned to the total of GI (GI %) (right).

Prophage

Prophage was analized using PHASTEST web.Then, prophages were identified in 74 complete genomes of Shewanella

Probiotic and pathogenic strains comparison

This analysis were focused on pathogenic and probiotic strains comparison by Tarsynflow, which identified the specific genes on pathogenic and their absent on probiotic strain.